Contacts of the strand formed by residues 102 - 107 (chain K) in PDB entry 1FSK


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with THR 102 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6K  GLN*     3.4    24.7    -      -       +      +
      7K  SER      5.0     1.6    -      -       -      +
      8K  PRO*     2.7    29.7    +      -       -      +
      9K  LYS      3.5     7.0    +      -       -      -
     10K  SER*     4.1     5.2    +      -       -      -
     11K  MET*     4.8     0.2    -      -       -      +
     21K  LEU*     3.3    39.6    -      -       +      +
     22K  SER      5.4     1.8    -      -       -      +
     85K  ASP*     3.2     3.9    +      -       -      -
     86K  TYR*     3.1    28.3    +      -       +      +
    101K  GLY*     1.3    74.1    -      -       -      -
    103K  LYS*     1.3    62.6    +      -       -      +
    104K  LEU      3.5     1.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 103 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9K  LYS      3.2    11.9    +      -       -      +
     10K  SER*     3.3     8.4    -      -       -      -
     11K  MET*     2.9    27.1    +      -       -      +
     21K  LEU*     6.1     0.2    -      -       -      -
     83K  LEU*     5.6     3.4    -      -       +      -
     84K  ALA      3.7    13.0    -      -       -      +
     85K  ASP*     3.6    14.1    +      -       +      +
    101K  GLY      4.2     0.2    -      -       -      -
    102K  THR*     1.3    70.5    -      -       -      +
    104K  LEU*     1.3    65.1    +      -       -      +
    105K  GLU*     3.6    39.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 104 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11K  MET*     3.7    22.4    -      -       +      +
     13K  VAL*     4.6     7.9    -      -       +      -
     19K  VAL*     4.3    24.5    -      -       +      -
     21K  LEU*     5.4     6.3    -      -       +      -
     75K  ILE*     4.0    20.0    -      -       +      -
     78K  VAL*     4.0    18.8    -      -       +      -
     82K  ASP      3.2    23.8    -      -       -      +
     83K  LEU*     2.7    33.3    -      -       -      +
     84K  ALA      2.8    19.1    +      -       -      +
     86K  TYR*     3.7    18.2    -      -       +      -
    102K  THR      3.5     1.8    +      -       -      +
    103K  LYS*     1.3    73.7    -      -       -      +
    105K  GLU*     1.3    58.3    +      -       -      +
    106K  ILE*     4.3     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 105 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10K  SER*     3.7    23.4    +      -       -      -
     11K  MET      2.6    16.1    +      -       -      +
     12K  SER*     2.9    41.7    +      -       -      +
     13K  VAL*     3.1     5.4    +      -       -      +
     83K  LEU*     4.0     1.1    -      -       +      -
    103K  LYS*     3.6    38.7    +      -       +      +
    104K  LEU*     1.3    78.5    -      -       -      +
    106K  ILE*     1.3    64.0    +      -       -      +
    166K  GLN*     3.7    10.7    -      -       -      +
    173K  TYR*     4.0    14.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 106 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12K  SER*     5.6     0.9    -      -       -      -
     13K  VAL*     3.2     9.6    -      -       +      +
     15K  VAL*     3.9    20.0    -      -       +      +
     78K  VAL*     4.5    10.5    -      -       +      -
     79K  GLN      3.1    13.2    -      -       -      +
     80K  ALA*     3.1    43.7    -      -       -      +
     83K  LEU*     4.0    17.2    -      -       +      +
    104K  LEU*     4.4     2.2    +      -       +      -
    105K  GLU*     1.3    73.9    -      -       -      +
    107K  LYS*     1.3    73.8    +      -       -      +
    108K  ARG*     4.2     0.4    +      -       +      -
    140K  TYR*     3.7     2.4    +      -       -      -
    166K  GLN*     2.3    39.6    +      -       -      +
    171K  SER*     3.4    24.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 107 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12K  SER*     5.0     8.3    -      -       -      +
     13K  VAL*     2.8    21.1    +      -       -      +
     14K  SER*     3.5    35.6    +      -       -      +
     15K  VAL*     4.2     3.3    +      -       -      +
    105K  GLU      3.9     0.2    +      -       -      -
    106K  ILE*     1.3    77.4    -      -       -      +
    108K  ARG*     1.3    73.6    +      -       -      +
    140K  TYR*     3.0    16.2    -      -       +      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il